The tick genus Haemaphysalis is represented by four species in the New World, of which only the species Haemaphysalis leporispalustris has been associated with Rickettsiae. The present study reports for the first time the presence of a Rickettsia strain in the tick Haemaphysalis juxtakochi. A free-living male of H. juxtakochi, collected in the state of Rondonia, Western Amazon, Brazil, was subjected to DNA extraction and tested by PCR targeting the four rickettsial genes: gltA, 17-kDa, ompA and ompB. The nucleotide sequences obtained from the PCR products were, by BLAST analyses, closest to Rickettsia rhipicephali sharing 99.7% (1147/1150), 98.8% (429/434), 99.0% (486/491) and 99.0% (809/817) identities with the partial sequences of the gltA, 17-kDa, ompA and ompB genes, respectively. Phylogenetic analyses inferred from the four rickettsial genes showed a high-degree of similarity of this H. juxtakochi-Rickettsia with R. rhipicephali. These two agents grouped together in all trees, always with high bootstrap support (75-96%). This study gives molecular evidence for the presence of a Rickettsia species, designated as strain R300, in the tick H. juxtakochi from the Western Amazon area of Brazil. Genetic analyses showed R300 to be closely related to R. rhipicephali.